I am running peptides identification and quantification on Maxquant version 188.8.131.52.
I found some enriched peptides showed 0 in their intensities in some samples using "match between runs" and "classic normalization", while some of the same peptides showed high intensity in other samples undergoing the same treatment procedure.
Can I suspect that the intensity calculation was done by an unknown "filtration" process? Does anybody know how to calculate the intensity from the Maxquant given parameters? Or does anyone know how I can manually check the intensity?